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Not sure what is going wrong here. Try running
mri_annotation2label --subject myatlas.i3 --hemi lh --outdir
/media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/make_cortex_label.tmp.8214
--annotation aparc.a2009s
Does it segfault in the
Yes, it is possible, but the inferior contrasts of these sequences compared to
FLAIR will likely yield noisier results.
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Ritobrato Datta
Reply-To: Freesurfer
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Hi All,
I have T1w MPRAGE, T2w and PD images but I dont have FLAIR images from
a Multiple Sclerosis study. Can I use samseg to segment the lesions ?
Can you please suggest ?
Many thanks
Ri
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Hi Douglas,
I found the aseg.presurf.mgz for all cross sessions and base using version
6.0.
Best,
Qi
On Sun, Apr 18, 2021 at 10:43 PM Douglas N. Greve
wrote:
> Check each of your cross time points to make sure that all have an
> aseg.presurf.mgz.
Hi Qi - This is documented here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Zeng, Qi
Sent: Monday, April 19, 2021 1:40 PM
To: Freesurfer support list
Subject:
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Hi Experts,
I understand there is surface-based group analysis in Freesurfer, which is
for thickness, curvature, volume and etc. Is there a group analysis for DTI
tracula results? Any links to recommend to conduct the analysis?
Thank you so much!
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Thank you Douglas for the answer. Could you be more explicit?
So, once you have the aseg.stats you need to run which command with --etiv-only?
On Mon, Apr 19, 2021 at 4:00 PM Douglas N. Greve
wrote:
> It is not done. If you are running
Hi Mason
Pretty much all surfaces of a single subject/hemi have the same topology
(number of vertices/faces/etc...), so if you map to any of them you map to all
of them.
As for the syntax for doing this in one step I defer to Doug. Doing it in 2
steps I would use the white or pial surface to
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Hi Bruce,
No problem. I tried to run vol2surf using the following command, but it doesn't
run.
* mri_vol2surf --mov filtered_func_data.nii.gz --hemi rh --reg
/home/masontwells/Documents/freesurfer/subjects/sub-0006/surf/rh.sphere.reg
Hi Mason
I should have read to the end of my inbox before replying - Doug is the expert
in this so I would definitely follow his advise over mine. In general the
native->average surface transform is stored in the ?h.sphere.reg files
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
Hi Ellen
The folding index is pretty sensitive to kmax, which can be huge for tiny
antennae and such. It may not be the right measure for what you are trying to
capture. You can always compute the curvatures with mris_curvature then
overlay them and see if there are outlier values, or find the
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What is your advice for me now? Should I abandon the approach or is there
anyway to dig deeper into it and solve the error?
From: "Douglas N. Greve"
Reply-To: Freesurfer support list
Date: Sunday, April 18, 2021 at 10:21 PM
To:
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Hi Bruce,
Thanks for the reply. Would you agree this is the optimal way to move from
native vol to fs_average? I am confident with moving to native surface. My
current pipeline for this is as follows. Anything here stick out that you think
I should
Hi Mason
Yes, you can use mri_vol2surf to go native vol->native surf, then mri_surf2surf
to go native surf->group surf
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Mason Wells
Sent: Monday, April 19, 2021 5:45 AM
To: Freesurfer support list ;
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Hi Doug,
I have the data both in its native functional space (e.g. filtered_func_data).
I also run bbregister so have the transformation matrix to register it to the
T1 (e.g. anat2exf.register.dat). Do you suggest running vol2surf on the
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I am using FreeSurfer formatted data, yes. I believe I am mapping to the
individual surface correctly, but can I double check you agree?
I am running bbregister to register the functional data to the T1 which appears
to do a good job:
*
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Hi experts,
Could we analyze FLAIR images using freesurfer without having T1 images?
Saurabh
The materials in this message are private and may contain Protected Healthcare
Information or other information of a
You should talk to them
On 4/19/2021 7:52 AM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:
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What is your advice for me now? Should I abandon the approach or is
there anyway to dig deeper into it and solve the error?
*From: *"Douglas N. Greve"
*Reply-To:
It is not done. If you are running asegstats2table, you can have it
perform the correction by adding --etiv to the command line
On 4/19/2021 7:41 AM, Jaime Gomez wrote:
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Hi,
Does the asegs.stats produced by recon_all have the volume estimates
of
If you have the data in the native functional space, then just
mri_vol2surf --mov func.nii --hemi rh --reg reg.lta --trgsubject
fsaverage --projfrac 0.5 --o rh.func.fsa.mgz
On 4/19/2021 5:23 AM, Mason Wells wrote:
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Hi Bruce,
I looked at the pial surfaces and WM by running this for the outlier
subjects:
freeview -v subject1/mri/T1.mgz \
subject1/mri/brainmask.mgz \
-f subject1/surf/lh.white:edgecolor=yellow \
subject1/surf/lh.pial:edgecolor=red \
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Hello FreeSurfer developers,
I am trying to apply longitudinal processing on T1w MRI data for two
timepoints (~8 months between the two TP) in adolescents in order to
perform vertex-based analyses.
I am following the online tutorial here for the
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I'm getting a repeated error with libjpeg.so.62. is there any known fix?
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Hi,
Does the asegs.stats produced by recon_all have the volume estimates of
subcortical structures adjusted by the eTIV?
I want to understand the effect of sex in the segmented structures. Should
normalize the volumes of aseg.stats (Vol/eTIV) or is
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What is most important is that you map to your individual’s surface (whether
that is in subject’s physical space or MNI space doesn’t matter so much). If
you are using FreeSurfer formatted data, others can suggest how to do this.
With
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HI Matt,
Thanks for the reply. Are you suggesting I go native volume > native surface >
fs_average? If so, can you recommend the best can I go from native to group
average surface?
Mason T Wells, MSc
PhD student
School of Optometry and Vision
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You would do that through the subject’s own surface. It does not work very
well to map data directly from the volume onto group average surfaces (see e.g.
Coalson et al., 2018 PNAS).
Matt.
From: on behalf of Mason Wells
Reply-To: Freesurfer
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Hi experts,
I have some fMRI data that I have pre-processed in Feat. I want to resample a
single subject's data to the fs_average surface but unsure of the most optimal
way of doing this. At present I am warping the functional data to the MNI brain
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